The two-year JGBs have faced headwinds as the Bank of Japan has recently been trimming its buying of bills and shorter-dated debt at regular JGB-buying operations in an attempt to improve market liquidity, which had practically dried up under its extensive easing scheme.

Selling by participants making room for Thursday's 2.2 trillion yen ($20.09 billion) five-year JGB auction also weighed on shorter-dated debt. The five-year yield rose 1 basis point to minus 0.100 percent, its highest since late February.

Long-end JGBs, on the other hand, took immediate cues from U.S. Treasuries, which saw their benchmark yield fall to seven-month lows overnight ahead of Thursday's general election in Britain, the European Central Bank's policy meeting, and former FBI Director James Comey's testimony before a Senate panel.

JGBs further out on the curve were also supported as the Bank of Japan conducted a regular debt-buying operation on Wednesday. The central bank bought 750 billion yen ($6.85 billion) of JGBs with maturities from 5 years to those exceeding 25 years.